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Status: Done started: 2020-Jun-08 14:50:37 UTC
Project NameNivolumab
SequenceQVQLVESGGGVVQPGRSLRLDCKASGITFSNSGMHWVRQAPGKGLEWVAVIWYDGSKRYY
Secondary structure

CEEEEEECCEEECCCCCEEEEEEEECCEEECCCEEEEEECCCCCEEEEEEEEECCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Jun-08 22:40 UTC

Time evolution of structural features: CABS energy, End-to-end distance and Radius of gyration.

Cluster #12345678910
Cluster density20.417.38.67.83.02.21.80.90.90.6
Cluster size828743553222171084
Average cluster RMSD4.05.05.07.110.69.89.210.78.77.1

Clustering of protein models is the task of separating a set of protein models (here a protein dynamics trajectory) into groups (called clusters). The clustering is done in such a way that models are more similar in the same group to each other (here in the sense of RMSD measure), than those in other groups (clusters). CABSfold utilizes classical K-means clustering method.
After clustering is done, each cluster representative is chosen (always the model which average dissimilarity to all models in a cluster is minimal). Predicted protein models, presented in the Predicted structures tab, are each cluster representatives (the clusters and the corresponding models are marked by the same numbers, e.g. Model 1 represents Cluster 1).
The clusters are numbered/ranked according to cluster density values, from the most dense (numbered as a first) to the least dense one.

#12345678910
1 0.00 4.70 7.09 6.73 12.10 15.70 14.00 13.60 15.20 17.10
2 4.70 0.00 8.34 7.47 12.40 15.50 13.70 13.70 15.00 17.80
3 7.09 8.34 0.00 9.11 12.80 15.30 13.90 16.10 17.60 18.00
4 6.73 7.47 9.11 0.00 12.90 15.20 13.10 12.90 16.40 14.60
5 12.10 12.40 12.80 12.90 0.00 11.10 11.50 12.90 12.80 15.70
6 15.70 15.50 15.30 15.20 11.10 0.00 7.22 13.20 17.10 13.60
7 14.00 13.70 13.90 13.10 11.50 7.22 0.00 11.40 15.90 13.30
8 13.60 13.70 16.10 12.90 12.90 13.20 11.40 0.00 12.30 11.80
9 15.20 15.00 17.60 16.40 12.80 17.10 15.90 12.30 0.00 19.80
10 17.10 17.80 18.00 14.60 15.70 13.60 13.30 11.80 19.80 0.00

The table contains RMSD values (calculated on the Cα atoms) between the predicted models.
Read more about the root-mean-square deviation (RMSD) measure.

#12345678910
1 1.00 0.78 0.38 0.44 0.26 0.26 0.26 0.27 0.22 0.31
2 0.78 1.00 0.33 0.46 0.23 0.24 0.25 0.26 0.22 0.29
3 0.38 0.33 1.00 0.29 0.25 0.20 0.23 0.24 0.24 0.23
4 0.44 0.46 0.29 1.00 0.20 0.26 0.27 0.24 0.22 0.28
5 0.26 0.23 0.25 0.20 1.00 0.32 0.29 0.25 0.26 0.23
6 0.26 0.24 0.20 0.26 0.32 1.00 0.34 0.26 0.26 0.25
7 0.26 0.25 0.23 0.27 0.29 0.34 1.00 0.28 0.25 0.25
8 0.27 0.26 0.24 0.24 0.25 0.26 0.28 1.00 0.27 0.22
9 0.22 0.22 0.24 0.22 0.26 0.26 0.25 0.27 1.00 0.22
10 0.31 0.29 0.23 0.28 0.23 0.25 0.25 0.22 0.22 1.00

The table contains GDT_TS values (calculated on the Cα atoms) between the predicted models.
Read more about the global distance test (GDT, also written as GDT_TS to represent "total score") measure.


 

© Laboratory of Theory of Biopolymers 2013